M01 Introduction to MD++

Manual 01 for MD++
Introduction to MD++

Keonwook Kang and Wei Cai

Nov 24 , 2007

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Overview

MD++ is a molecular dynamics simulation package written in C++. It is originally developed by Wei Cai when he was a graduate student at MIT and still being updated to include more features. MD++ is supposed to run in a Unix/Linux environment. However, if you have cygwin, a linux-like environment installed in your Windows machine, you can also enjoy MD++ there. Currently, this code is designed mainly for studying the atomic behavior in solid crystal materials. It can also be extended to study other systems, such as fluids, polymers and bio-molecules. This document is the first of a series of manuals written for those new to MD simulations. These manuals explain how to use MD++ with simple examples.

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Installation

The latest version of MD++ code can be downloaded from the web site, http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/. Here we assume that the reader is familiar with basic Unix/Linux shell commands. Before you download MD++ code, we recommend that you make a sub-directory Codes in your home directory.

$ mkdir Codes 
$ cd Codes 

Save the MD++ package in this directory(~/Codes). Suppose the downloaded file is md++-2007-01-07.tar.gz, then we can extract it by,

$ tar -zxvf md++-2007-01-07.tar.gz 

This command creates the MD++ sub-directory and extracts all the files into it. Go to the MD++ directory and make a runs directory if it does not exist.

$ cd MD++; mkdir runs 

To compile the codes in release(R) mode in a Linux system, type

$ make all build=R 

In order to compile MD++ In a different system (such as Windows), you can specify the SYS variable in the command line, such as

$ make all build=R SYS=cygwin 

provided that cygwin is installed. You can also compile MD++ code in an Apple/Machintosh computer, using

$ make all SYS=mac build=R 

By default, SYS=gpp which corresponds to the GNU c++ compiler. If you have the intel c/c++ compiler icc in your system, use SYS=intel to activate icc, which produces much faster executables than GNU c++ compiler. For more SYS values, take a look at the file ~/Codes/MD++/src/Makefie.base.

You may get an TCL-related error during compilation. You can bypass this error using, e.g.

$make SYS=cygwin TCL=no 

by suppressing TCL option.

After compilation, you have executable files such as fs_gpp, eam_gpp, and sw_gpp in the bin directory.<A NAME="tex2html5"

 HREF="footnode.html#foot152">5</A>If you just want to compile one executable file, such as fs_gpp, use 

$ make fs build=R 

The name of each execution file stands for the potential model used in the MD simulation. For example, fs stands for the Finnis-Sinclair (FS) potential [<A

HREF="node6.html#fin:sin">2</A>], lj for the

Lennard-Jones (LJ) pair potential [<A

HREF="node6.html#lj">3</A>], eam for the

embedded-atom method (EAM) potential [<A

HREF="node6.html#daw:bask">4</A>], and sw

for the Stillinger-Weber (SW) potential [<A

HREF="node6.html#sti:web">5</A>,<A
HREF="node6.html#bal:hal:til">6</A>]. Each potential model is

applicable to a set of atomic species. For example, the FS potential was designed for body-centered-cubic (BCC) metals such as Mo, Ta and W. The SW potential was designed for diamond-cubic semiconductors such as Si and Ge. The executable, md_gpp does not contain any potential model. Hence it cannot be used to compute any material properties but it can still be used to display atomic structures.
If you modify the source code (in the src directory), you need to recompile MD++. we recommend you to clean the previous executables and rebuild by,
$ make clean; make all build=R

To see more help on make, type
$ make help

To check if the installation and compilation is successful, try to run a script in the Examples directory, e.g.
$ bin/fs_gpp scripts/Examples/example01-mo.script

If you want to stop an MD++ run, press ctrl+c or close the visualization window.

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